Starting phenix.real_space_refine on Tue May 13 02:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162.map" model { file = "/net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rgx_19162/05_2025/8rgx_19162_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 6216 2.51 5 N 1764 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "L" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 5.62, per 1000 atoms: 0.57 Number of scatterers: 9924 At special positions: 0 Unit cell: (117.3, 117.3, 62.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1920 8.00 N 1764 7.00 C 6216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 43 through 64 removed outlier: 3.726A pdb=" N VAL A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 140 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.509A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 removed outlier: 3.741A pdb=" N VAL B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 88 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 111 through 140 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 43 through 64 removed outlier: 3.717A pdb=" N VAL C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 88 Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 111 through 140 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 43 through 64 removed outlier: 3.726A pdb=" N VAL D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 111 through 140 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.513A pdb=" N VAL E 41 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 64 removed outlier: 3.740A pdb=" N VAL E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 88 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 111 through 140 Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 43 through 64 removed outlier: 3.719A pdb=" N VAL F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 88 Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 111 through 140 Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 64 removed outlier: 3.724A pdb=" N VAL G 47 " --> pdb=" O GLN G 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 88 Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 111 through 140 Processing helix chain 'H' and resid 37 through 41 removed outlier: 3.512A pdb=" N VAL H 41 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 64 removed outlier: 3.741A pdb=" N VAL H 47 " --> pdb=" O GLN H 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 88 Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 111 through 140 Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'I' and resid 43 through 64 removed outlier: 3.717A pdb=" N VAL I 47 " --> pdb=" O GLN I 43 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 64 " --> pdb=" O GLU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 88 Processing helix chain 'I' and resid 90 through 101 Processing helix chain 'I' and resid 111 through 140 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 43 through 64 removed outlier: 3.725A pdb=" N VAL J 47 " --> pdb=" O GLN J 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 88 Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'J' and resid 111 through 140 Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.513A pdb=" N VAL K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 64 removed outlier: 3.744A pdb=" N VAL K 47 " --> pdb=" O GLN K 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 88 Processing helix chain 'K' and resid 90 through 101 Processing helix chain 'K' and resid 111 through 140 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 43 through 64 removed outlier: 3.716A pdb=" N VAL L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 64 " --> pdb=" O GLU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 88 Processing helix chain 'L' and resid 90 through 101 Processing helix chain 'L' and resid 111 through 140 836 hydrogen bonds defined for protein. 2448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3528 1.34 - 1.46: 1011 1.46 - 1.57: 5469 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 10056 Sorted by residual: bond pdb=" CB LEU F 74 " pdb=" CG LEU F 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.54e-01 bond pdb=" CB LEU C 74 " pdb=" CG LEU C 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.39e-01 bond pdb=" CB LEU L 74 " pdb=" CG LEU L 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.38e-01 bond pdb=" CB LEU B 74 " pdb=" CG LEU B 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.26e-01 bond pdb=" CB LEU K 74 " pdb=" CG LEU K 74 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.26e-01 ... (remaining 10051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 12552 0.77 - 1.54: 850 1.54 - 2.31: 129 2.31 - 3.09: 62 3.09 - 3.86: 27 Bond angle restraints: 13620 Sorted by residual: angle pdb=" C MET E 48 " pdb=" N ARG E 49 " pdb=" CA ARG E 49 " ideal model delta sigma weight residual 120.29 118.36 1.93 1.42e+00 4.96e-01 1.85e+00 angle pdb=" N GLY B 88 " pdb=" CA GLY B 88 " pdb=" C GLY B 88 " ideal model delta sigma weight residual 113.18 116.40 -3.22 2.37e+00 1.78e-01 1.84e+00 angle pdb=" N GLY K 88 " pdb=" CA GLY K 88 " pdb=" C GLY K 88 " ideal model delta sigma weight residual 113.18 116.39 -3.21 2.37e+00 1.78e-01 1.84e+00 angle pdb=" C MET I 48 " pdb=" N ARG I 49 " pdb=" CA ARG I 49 " ideal model delta sigma weight residual 120.29 118.37 1.92 1.42e+00 4.96e-01 1.84e+00 angle pdb=" C MET L 48 " pdb=" N ARG L 49 " pdb=" CA ARG L 49 " ideal model delta sigma weight residual 120.29 118.37 1.92 1.42e+00 4.96e-01 1.84e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 5553 12.81 - 25.63: 563 25.63 - 38.44: 100 38.44 - 51.26: 28 51.26 - 64.07: 20 Dihedral angle restraints: 6264 sinusoidal: 2616 harmonic: 3648 Sorted by residual: dihedral pdb=" CA ARG G 75 " pdb=" CB ARG G 75 " pdb=" CG ARG G 75 " pdb=" CD ARG G 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.43 -58.57 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG J 75 " pdb=" CB ARG J 75 " pdb=" CG ARG J 75 " pdb=" CD ARG J 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.44 -58.56 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 75 " pdb=" CB ARG A 75 " pdb=" CG ARG A 75 " pdb=" CD ARG A 75 " ideal model delta sinusoidal sigma weight residual -180.00 -121.44 -58.56 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 977 0.025 - 0.049: 454 0.049 - 0.074: 100 0.074 - 0.099: 47 0.099 - 0.123: 18 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL G 109 " pdb=" N VAL G 109 " pdb=" C VAL G 109 " pdb=" CB VAL G 109 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1593 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 43 " 0.014 5.00e-02 4.00e+02 2.19e-02 7.65e-01 pdb=" N PRO H 44 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 43 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.53e-01 pdb=" N PRO B 44 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN K 43 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.45e-01 pdb=" N PRO K 44 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO K 44 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 44 " 0.012 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2818 2.83 - 3.35: 10090 3.35 - 3.87: 16023 3.87 - 4.38: 18281 4.38 - 4.90: 32429 Nonbonded interactions: 79641 Sorted by model distance: nonbonded pdb=" NH1 ARG F 116 " pdb=" OE2 GLU G 60 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG C 116 " pdb=" OE2 GLU D 60 " model vdw 2.317 3.120 nonbonded pdb=" OE2 GLU A 60 " pdb=" NH1 ARG L 116 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG I 116 " pdb=" OE2 GLU J 60 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASP K 67 " pdb=" OG SER K 70 " model vdw 2.323 3.040 ... (remaining 79636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 10056 Z= 0.160 Angle : 0.480 3.858 13620 Z= 0.258 Chirality : 0.033 0.123 1596 Planarity : 0.004 0.022 1812 Dihedral : 11.005 64.071 3864 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.76 % Allowed : 4.73 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.23), residues: 1236 helix: 2.20 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : 0.23 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 125 HIS 0.002 0.001 HIS K 131 PHE 0.004 0.001 PHE E 138 ARG 0.003 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.13469 ( 836) hydrogen bonds : angle 3.54709 ( 2448) covalent geometry : bond 0.00357 (10056) covalent geometry : angle 0.47991 (13620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 397 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7172 (mmm160) REVERT: B 55 LYS cc_start: 0.8235 (tttp) cc_final: 0.7975 (tttp) REVERT: B 73 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7629 (tpt170) REVERT: B 121 GLN cc_start: 0.8482 (tt0) cc_final: 0.8239 (tt0) REVERT: C 46 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7929 (ttmt) REVERT: C 73 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7048 (mmm160) REVERT: C 84 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 73 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7166 (mmm160) REVERT: E 55 LYS cc_start: 0.8235 (tttp) cc_final: 0.8016 (tttp) REVERT: E 73 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7629 (tpt170) REVERT: E 121 GLN cc_start: 0.8484 (tt0) cc_final: 0.8234 (tt0) REVERT: F 46 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7932 (ttmt) REVERT: F 73 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7045 (mmm160) REVERT: F 84 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 73 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7163 (mmm160) REVERT: H 55 LYS cc_start: 0.8234 (tttp) cc_final: 0.7972 (tttp) REVERT: H 73 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7633 (tpt170) REVERT: H 121 GLN cc_start: 0.8485 (tt0) cc_final: 0.8239 (tt0) REVERT: I 46 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7930 (ttmt) REVERT: I 73 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7047 (mmm160) REVERT: I 84 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7421 (mm-30) REVERT: J 73 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7177 (mmm160) REVERT: K 55 LYS cc_start: 0.8233 (tttp) cc_final: 0.8016 (tttp) REVERT: K 121 GLN cc_start: 0.8485 (tt0) cc_final: 0.8243 (tt0) REVERT: L 46 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7931 (ttmt) REVERT: L 73 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7041 (mmm160) REVERT: L 84 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7429 (mm-30) outliers start: 8 outliers final: 8 residues processed: 397 average time/residue: 0.2712 time to fit residues: 140.4184 Evaluate side-chains 323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 315 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain L residue 82 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 119 GLN C 119 GLN D 119 GLN E 119 GLN F 119 GLN G 119 GLN H 119 GLN I 119 GLN J 119 GLN K 119 GLN L 119 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126290 restraints weight = 13908.979| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.06 r_work: 0.3266 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10056 Z= 0.131 Angle : 0.491 4.003 13620 Z= 0.263 Chirality : 0.031 0.111 1596 Planarity : 0.004 0.026 1812 Dihedral : 3.866 26.191 1372 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.46 % Allowed : 9.09 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.22), residues: 1236 helix: 2.89 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : 0.37 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 125 HIS 0.001 0.000 HIS G 78 PHE 0.003 0.001 PHE E 104 ARG 0.008 0.001 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 836) hydrogen bonds : angle 3.07967 ( 2448) covalent geometry : bond 0.00272 (10056) covalent geometry : angle 0.49141 (13620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7153 (mmm160) REVERT: A 116 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8170 (mtm110) REVERT: B 42 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 46 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8088 (tttt) REVERT: B 55 LYS cc_start: 0.8540 (tttp) cc_final: 0.8319 (tttm) REVERT: B 73 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7309 (mmm160) REVERT: C 72 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: C 73 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7205 (mmm160) REVERT: D 73 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7152 (mmm160) REVERT: D 116 ARG cc_start: 0.8482 (mtm110) cc_final: 0.8173 (mtm110) REVERT: E 42 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7595 (mt-10) REVERT: E 46 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8086 (tttt) REVERT: E 55 LYS cc_start: 0.8534 (tttp) cc_final: 0.8254 (tttm) REVERT: E 73 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7279 (mmm160) REVERT: F 72 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: F 73 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7196 (mmm160) REVERT: F 94 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7792 (ttm170) REVERT: G 73 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7135 (mmm160) REVERT: G 116 ARG cc_start: 0.8472 (mtm110) cc_final: 0.8162 (mtm110) REVERT: H 46 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8082 (tttt) REVERT: H 55 LYS cc_start: 0.8529 (tttp) cc_final: 0.8309 (tttm) REVERT: H 73 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7620 (tpt170) REVERT: I 72 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: I 73 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7185 (mmm160) REVERT: I 94 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7811 (ttm170) REVERT: J 73 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7153 (mmm160) REVERT: J 116 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8157 (mtm110) REVERT: K 46 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8081 (tttt) REVERT: K 55 LYS cc_start: 0.8564 (tttp) cc_final: 0.8284 (tttm) REVERT: K 73 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7622 (tpt170) REVERT: L 72 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: L 73 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7205 (mmm160) outliers start: 26 outliers final: 13 residues processed: 364 average time/residue: 0.2781 time to fit residues: 131.1194 Evaluate side-chains 313 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN D 119 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN J 119 GLN ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124521 restraints weight = 13808.481| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.21 r_work: 0.3245 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10056 Z= 0.125 Angle : 0.480 4.193 13620 Z= 0.253 Chirality : 0.031 0.117 1596 Planarity : 0.004 0.028 1812 Dihedral : 3.243 13.008 1356 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.64 % Allowed : 10.32 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.26 (0.23), residues: 1236 helix: 3.17 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -0.08 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 125 HIS 0.001 0.001 HIS D 78 PHE 0.003 0.001 PHE K 138 ARG 0.005 0.001 ARG I 75 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 836) hydrogen bonds : angle 2.94905 ( 2448) covalent geometry : bond 0.00267 (10056) covalent geometry : angle 0.48039 (13620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8501 (mtp85) cc_final: 0.7200 (mmm160) REVERT: A 76 ASP cc_start: 0.8373 (m-30) cc_final: 0.8020 (m-30) REVERT: A 116 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8296 (mtp-110) REVERT: B 42 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 46 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8070 (tttt) REVERT: B 55 LYS cc_start: 0.8502 (tttp) cc_final: 0.8291 (tttm) REVERT: B 60 GLU cc_start: 0.7706 (tp30) cc_final: 0.7478 (tp30) REVERT: B 73 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7601 (tpt170) REVERT: C 42 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 60 GLU cc_start: 0.7394 (tp30) cc_final: 0.7079 (tp30) REVERT: C 73 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7135 (mmm160) REVERT: C 94 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7677 (ttm170) REVERT: D 73 ARG cc_start: 0.8493 (mtp85) cc_final: 0.7212 (mmm160) REVERT: D 76 ASP cc_start: 0.8369 (m-30) cc_final: 0.8024 (m-30) REVERT: D 116 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8299 (mtp-110) REVERT: E 42 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7705 (mt-10) REVERT: E 46 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8057 (tttt) REVERT: E 55 LYS cc_start: 0.8484 (tttp) cc_final: 0.8279 (tttm) REVERT: E 60 GLU cc_start: 0.7701 (tp30) cc_final: 0.7480 (tp30) REVERT: E 73 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7590 (tpt170) REVERT: F 72 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8055 (m-40) REVERT: F 73 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7154 (mmm160) REVERT: F 94 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7658 (ttm170) REVERT: G 73 ARG cc_start: 0.8510 (mtp85) cc_final: 0.7222 (mmm160) REVERT: G 76 ASP cc_start: 0.8369 (m-30) cc_final: 0.8022 (m-30) REVERT: G 116 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8309 (mtp-110) REVERT: H 46 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8047 (tttt) REVERT: H 55 LYS cc_start: 0.8488 (tttp) cc_final: 0.8281 (tttm) REVERT: H 60 GLU cc_start: 0.7713 (tp30) cc_final: 0.7495 (tp30) REVERT: H 73 ARG cc_start: 0.8382 (mtp85) cc_final: 0.7604 (tpt170) REVERT: I 72 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: I 73 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7164 (mmm160) REVERT: I 94 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7674 (ttm170) REVERT: J 73 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7236 (mmm160) REVERT: J 76 ASP cc_start: 0.8350 (m-30) cc_final: 0.8000 (m-30) REVERT: J 116 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8241 (mtp-110) REVERT: K 46 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8071 (tttt) REVERT: K 55 LYS cc_start: 0.8478 (tttp) cc_final: 0.8268 (tttm) REVERT: K 73 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7594 (tpt170) REVERT: L 42 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7496 (mt-10) REVERT: L 72 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: L 73 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7141 (mmm160) outliers start: 49 outliers final: 30 residues processed: 327 average time/residue: 0.2685 time to fit residues: 114.6656 Evaluate side-chains 310 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** K 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.158454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125339 restraints weight = 13550.161| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.21 r_work: 0.3256 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10056 Z= 0.116 Angle : 0.457 3.969 13620 Z= 0.243 Chirality : 0.030 0.113 1596 Planarity : 0.004 0.034 1812 Dihedral : 3.171 12.635 1356 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.17 % Allowed : 11.74 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.06 (0.22), residues: 1236 helix: 3.87 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.60 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 125 HIS 0.001 0.000 HIS A 78 PHE 0.003 0.001 PHE B 138 ARG 0.005 0.000 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 836) hydrogen bonds : angle 2.83878 ( 2448) covalent geometry : bond 0.00244 (10056) covalent geometry : angle 0.45729 (13620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 72 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7664 (m110) REVERT: A 73 ARG cc_start: 0.8519 (mtp85) cc_final: 0.7223 (mmm160) REVERT: A 76 ASP cc_start: 0.8284 (m-30) cc_final: 0.7933 (m-30) REVERT: A 116 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8091 (mtp-110) REVERT: B 42 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7711 (mt-10) REVERT: B 46 LYS cc_start: 0.8316 (ttmt) cc_final: 0.8071 (tttt) REVERT: B 55 LYS cc_start: 0.8490 (tttp) cc_final: 0.8278 (tttm) REVERT: B 73 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7593 (tpt170) REVERT: C 42 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 73 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7129 (mmm160) REVERT: C 94 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7721 (ttm170) REVERT: D 68 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7019 (tm-30) REVERT: D 72 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7682 (m110) REVERT: D 73 ARG cc_start: 0.8512 (mtp85) cc_final: 0.7217 (mmm160) REVERT: D 76 ASP cc_start: 0.8301 (m-30) cc_final: 0.7950 (m-30) REVERT: D 116 ARG cc_start: 0.8543 (mtm110) cc_final: 0.8092 (mtp-110) REVERT: E 42 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7698 (mt-10) REVERT: E 46 LYS cc_start: 0.8300 (ttmt) cc_final: 0.8054 (tttt) REVERT: E 55 LYS cc_start: 0.8452 (tttp) cc_final: 0.8249 (tttm) REVERT: E 73 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7604 (tpt170) REVERT: F 72 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8040 (m-40) REVERT: F 73 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7136 (mmm160) REVERT: F 94 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7620 (ttm170) REVERT: G 68 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6999 (tm-30) REVERT: G 72 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7668 (m110) REVERT: G 73 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7132 (mmm160) REVERT: G 76 ASP cc_start: 0.8276 (m-30) cc_final: 0.7924 (m-30) REVERT: G 116 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8098 (mtp-110) REVERT: H 46 LYS cc_start: 0.8311 (ttmt) cc_final: 0.8079 (tttt) REVERT: H 55 LYS cc_start: 0.8460 (tttp) cc_final: 0.8248 (tttm) REVERT: H 73 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7608 (tpt170) REVERT: I 72 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8033 (m-40) REVERT: I 73 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7112 (mmm160) REVERT: I 94 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7652 (ttm170) REVERT: J 42 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7545 (mt-10) REVERT: J 72 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7716 (m110) REVERT: J 73 ARG cc_start: 0.8509 (mtp85) cc_final: 0.7226 (mmm160) REVERT: J 76 ASP cc_start: 0.8278 (m-30) cc_final: 0.7900 (m-30) REVERT: J 116 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8079 (mtp-110) REVERT: K 46 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8084 (tttt) REVERT: K 55 LYS cc_start: 0.8446 (tttp) cc_final: 0.8234 (tttm) REVERT: K 73 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7594 (tpt170) REVERT: L 42 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7544 (mt-10) REVERT: L 72 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (m-40) REVERT: L 73 ARG cc_start: 0.8309 (mtp85) cc_final: 0.7121 (mmm160) outliers start: 44 outliers final: 30 residues processed: 338 average time/residue: 0.2756 time to fit residues: 122.8054 Evaluate side-chains 329 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 119 GLN C 119 GLN D 119 GLN E 119 GLN F 119 GLN G 119 GLN H 119 GLN I 119 GLN J 119 GLN K 119 GLN L 119 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126613 restraints weight = 13866.650| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.08 r_work: 0.3277 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10056 Z= 0.115 Angle : 0.464 4.212 13620 Z= 0.246 Chirality : 0.031 0.111 1596 Planarity : 0.004 0.020 1812 Dihedral : 3.134 12.485 1356 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.88 % Allowed : 13.54 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.22), residues: 1236 helix: 3.95 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.65 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 125 HIS 0.001 0.000 HIS J 78 PHE 0.002 0.001 PHE K 138 ARG 0.004 0.000 ARG K 75 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 836) hydrogen bonds : angle 2.77568 ( 2448) covalent geometry : bond 0.00240 (10056) covalent geometry : angle 0.46446 (13620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7433 (tp30) cc_final: 0.7206 (tp30) REVERT: A 68 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7019 (tm-30) REVERT: A 72 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7663 (m110) REVERT: A 73 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7179 (mmm160) REVERT: A 76 ASP cc_start: 0.8176 (m-30) cc_final: 0.7846 (m-30) REVERT: A 116 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8174 (mtm110) REVERT: B 46 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8097 (tttt) REVERT: B 55 LYS cc_start: 0.8572 (tttp) cc_final: 0.8358 (tttm) REVERT: B 73 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7622 (tpt170) REVERT: B 92 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5783 (tm-30) REVERT: C 42 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7372 (mt-10) REVERT: C 73 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7177 (mmm160) REVERT: D 68 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7052 (tm-30) REVERT: D 72 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7673 (m110) REVERT: D 73 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7154 (mmm160) REVERT: D 76 ASP cc_start: 0.8178 (m-30) cc_final: 0.7844 (m-30) REVERT: D 116 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8160 (mtm110) REVERT: E 46 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8073 (tttt) REVERT: E 55 LYS cc_start: 0.8587 (tttp) cc_final: 0.8372 (tttm) REVERT: E 73 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7623 (tpt170) REVERT: E 92 GLU cc_start: 0.6064 (tm-30) cc_final: 0.5814 (tm-30) REVERT: F 73 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7182 (mmm160) REVERT: F 94 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7778 (ttm170) REVERT: G 68 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7066 (tm-30) REVERT: G 72 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7666 (m110) REVERT: G 73 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7057 (mmm160) REVERT: G 76 ASP cc_start: 0.8174 (m-30) cc_final: 0.7837 (m-30) REVERT: G 116 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8164 (mtm110) REVERT: H 46 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8090 (tttt) REVERT: H 55 LYS cc_start: 0.8566 (tttp) cc_final: 0.8346 (tttm) REVERT: H 73 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7611 (tpt170) REVERT: H 92 GLU cc_start: 0.5979 (tm-30) cc_final: 0.5729 (tm-30) REVERT: I 73 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7198 (mmm160) REVERT: I 94 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7790 (ttm170) REVERT: J 68 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7057 (tm-30) REVERT: J 72 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7578 (m110) REVERT: J 73 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7031 (mmm160) REVERT: J 76 ASP cc_start: 0.8244 (m-30) cc_final: 0.7914 (m-30) REVERT: J 116 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8155 (mtm110) REVERT: K 46 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8087 (tttt) REVERT: K 55 LYS cc_start: 0.8555 (tttp) cc_final: 0.8340 (tttm) REVERT: K 73 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7615 (tpt170) REVERT: K 92 GLU cc_start: 0.6062 (tm-30) cc_final: 0.5835 (tm-30) REVERT: L 72 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: L 73 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7183 (mmm160) outliers start: 41 outliers final: 32 residues processed: 348 average time/residue: 0.2682 time to fit residues: 120.7140 Evaluate side-chains 331 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125015 restraints weight = 13867.552| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.07 r_work: 0.3250 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10056 Z= 0.135 Angle : 0.516 7.837 13620 Z= 0.265 Chirality : 0.032 0.141 1596 Planarity : 0.004 0.023 1812 Dihedral : 3.151 12.652 1356 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.36 % Allowed : 13.54 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.08 (0.22), residues: 1236 helix: 3.88 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.62 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 125 HIS 0.001 0.001 HIS K 78 PHE 0.004 0.001 PHE B 130 ARG 0.003 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 836) hydrogen bonds : angle 2.79945 ( 2448) covalent geometry : bond 0.00299 (10056) covalent geometry : angle 0.51635 (13620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7747 (m110) REVERT: A 73 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7150 (mmm160) REVERT: A 76 ASP cc_start: 0.8178 (m-30) cc_final: 0.7833 (m-30) REVERT: A 116 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8167 (mtm110) REVERT: B 46 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8162 (tttt) REVERT: B 55 LYS cc_start: 0.8613 (tttp) cc_final: 0.8386 (tttm) REVERT: B 73 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7635 (tpt170) REVERT: C 73 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7214 (mmm160) REVERT: C 94 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7898 (ttm170) REVERT: D 72 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7767 (m110) REVERT: D 73 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7144 (mmm160) REVERT: D 76 ASP cc_start: 0.8194 (m-30) cc_final: 0.7855 (m-30) REVERT: D 116 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8148 (mtm110) REVERT: E 46 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8140 (tttt) REVERT: E 55 LYS cc_start: 0.8616 (tttp) cc_final: 0.8393 (tttm) REVERT: E 73 ARG cc_start: 0.8377 (mtp85) cc_final: 0.7631 (tpt170) REVERT: F 72 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8080 (m-40) REVERT: F 73 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7199 (mmm160) REVERT: F 94 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7803 (ttm170) REVERT: G 72 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7769 (m110) REVERT: G 73 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7123 (mmm160) REVERT: G 76 ASP cc_start: 0.8204 (m-30) cc_final: 0.7863 (m-30) REVERT: G 116 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8129 (mtm110) REVERT: H 46 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8164 (tttt) REVERT: H 55 LYS cc_start: 0.8581 (tttp) cc_final: 0.8352 (tttm) REVERT: H 73 ARG cc_start: 0.8394 (mtp85) cc_final: 0.7660 (tpt170) REVERT: I 72 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: I 73 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7210 (mmm160) REVERT: I 94 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7813 (ttm170) REVERT: J 72 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7725 (m110) REVERT: J 73 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7106 (mmm160) REVERT: J 76 ASP cc_start: 0.8280 (m-30) cc_final: 0.7938 (m-30) REVERT: J 116 ARG cc_start: 0.8399 (mtm110) cc_final: 0.8150 (mtm110) REVERT: K 46 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8156 (tttt) REVERT: K 55 LYS cc_start: 0.8598 (tttp) cc_final: 0.8377 (tttm) REVERT: K 73 ARG cc_start: 0.8394 (mtp85) cc_final: 0.7622 (tpt170) REVERT: L 72 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: L 73 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7197 (mmm160) REVERT: L 94 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7861 (ttm170) outliers start: 46 outliers final: 39 residues processed: 310 average time/residue: 0.2792 time to fit residues: 111.9499 Evaluate side-chains 311 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126270 restraints weight = 14094.123| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.12 r_work: 0.3268 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10056 Z= 0.118 Angle : 0.505 5.387 13620 Z= 0.264 Chirality : 0.031 0.122 1596 Planarity : 0.003 0.021 1812 Dihedral : 3.143 12.574 1356 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.60 % Allowed : 16.19 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.21 (0.22), residues: 1236 helix: 4.00 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.51 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 125 HIS 0.001 0.000 HIS G 78 PHE 0.002 0.000 PHE L 138 ARG 0.003 0.000 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 836) hydrogen bonds : angle 2.72923 ( 2448) covalent geometry : bond 0.00249 (10056) covalent geometry : angle 0.50464 (13620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7773 (m110) REVERT: A 73 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7127 (mmm160) REVERT: A 76 ASP cc_start: 0.8160 (m-30) cc_final: 0.7859 (m-30) REVERT: B 46 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8075 (tttt) REVERT: B 55 LYS cc_start: 0.8580 (tttp) cc_final: 0.8367 (tttm) REVERT: B 73 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7625 (tpt170) REVERT: C 73 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7183 (mmm160) REVERT: D 72 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7774 (m110) REVERT: D 73 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7122 (mmm160) REVERT: D 76 ASP cc_start: 0.8182 (m-30) cc_final: 0.7882 (m-30) REVERT: E 46 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8113 (tttt) REVERT: E 55 LYS cc_start: 0.8584 (tttp) cc_final: 0.8370 (tttm) REVERT: E 73 ARG cc_start: 0.8383 (mtp85) cc_final: 0.7626 (tpt170) REVERT: F 72 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8093 (m-40) REVERT: F 73 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7198 (mmm160) REVERT: F 94 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7779 (ttm170) REVERT: G 72 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7776 (m110) REVERT: G 73 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7107 (mmm160) REVERT: G 76 ASP cc_start: 0.8187 (m-30) cc_final: 0.7883 (m-30) REVERT: H 46 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8139 (tttt) REVERT: H 55 LYS cc_start: 0.8538 (tttp) cc_final: 0.8309 (tttm) REVERT: H 73 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7612 (tpt170) REVERT: I 73 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7206 (mmm160) REVERT: I 94 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7792 (ttm170) REVERT: J 72 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7707 (m110) REVERT: J 73 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7057 (mmm160) REVERT: J 76 ASP cc_start: 0.8268 (m-30) cc_final: 0.7923 (m-30) REVERT: K 46 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8136 (tttt) REVERT: K 55 LYS cc_start: 0.8553 (tttp) cc_final: 0.8351 (tttm) REVERT: K 73 ARG cc_start: 0.8409 (mtp85) cc_final: 0.7614 (tpt170) REVERT: L 72 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: L 73 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7194 (mmm160) outliers start: 38 outliers final: 28 residues processed: 305 average time/residue: 0.2888 time to fit residues: 113.1430 Evaluate side-chains 301 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126040 restraints weight = 13891.717| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.11 r_work: 0.3263 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10056 Z= 0.122 Angle : 0.517 6.093 13620 Z= 0.273 Chirality : 0.032 0.132 1596 Planarity : 0.003 0.021 1812 Dihedral : 3.136 12.763 1356 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.41 % Allowed : 17.42 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.14 (0.22), residues: 1236 helix: 3.96 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.41 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 125 HIS 0.001 0.000 HIS H 78 PHE 0.002 0.001 PHE K 138 ARG 0.004 0.000 ARG J 94 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 836) hydrogen bonds : angle 2.73635 ( 2448) covalent geometry : bond 0.00260 (10056) covalent geometry : angle 0.51746 (13620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7768 (m110) REVERT: A 73 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7099 (mmm160) REVERT: A 76 ASP cc_start: 0.8149 (m-30) cc_final: 0.7836 (m-30) REVERT: B 46 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8105 (tttt) REVERT: B 55 LYS cc_start: 0.8608 (tttp) cc_final: 0.8376 (tttm) REVERT: B 60 GLU cc_start: 0.7557 (tp30) cc_final: 0.7262 (tp30) REVERT: B 73 ARG cc_start: 0.8394 (mtp85) cc_final: 0.7658 (tpt170) REVERT: C 73 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7656 (tpt170) REVERT: D 72 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7737 (m110) REVERT: D 73 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7097 (mmm160) REVERT: D 76 ASP cc_start: 0.8168 (m-30) cc_final: 0.7856 (m-30) REVERT: E 46 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8114 (tttt) REVERT: E 55 LYS cc_start: 0.8591 (tttp) cc_final: 0.8365 (tttm) REVERT: E 60 GLU cc_start: 0.7621 (tp30) cc_final: 0.7352 (tp30) REVERT: E 73 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7652 (tpt170) REVERT: F 73 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7199 (mmm160) REVERT: F 94 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7775 (ttm170) REVERT: G 72 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7778 (m110) REVERT: G 73 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7096 (mmm160) REVERT: G 76 ASP cc_start: 0.8171 (m-30) cc_final: 0.7858 (m-30) REVERT: H 46 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8117 (tttt) REVERT: H 55 LYS cc_start: 0.8558 (tttp) cc_final: 0.8328 (tttm) REVERT: H 60 GLU cc_start: 0.7601 (tp30) cc_final: 0.7325 (tp30) REVERT: H 73 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7643 (tpt170) REVERT: I 73 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7208 (mmm160) REVERT: I 94 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7803 (ttm170) REVERT: J 72 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7686 (m110) REVERT: J 73 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7041 (mmm160) REVERT: J 76 ASP cc_start: 0.8253 (m-30) cc_final: 0.7901 (m-30) REVERT: K 55 LYS cc_start: 0.8591 (tttp) cc_final: 0.8366 (tttm) REVERT: K 73 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7600 (tpt170) REVERT: L 73 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7183 (mmm160) REVERT: L 94 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7838 (ttm170) outliers start: 36 outliers final: 31 residues processed: 300 average time/residue: 0.2569 time to fit residues: 100.8515 Evaluate side-chains 308 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125550 restraints weight = 13928.735| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.11 r_work: 0.3261 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10056 Z= 0.129 Angle : 0.537 8.496 13620 Z= 0.284 Chirality : 0.032 0.118 1596 Planarity : 0.004 0.022 1812 Dihedral : 3.119 12.952 1356 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.22 % Allowed : 18.37 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.13 (0.21), residues: 1236 helix: 3.96 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.40 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 125 HIS 0.001 0.000 HIS B 78 PHE 0.002 0.001 PHE C 130 ARG 0.005 0.000 ARG J 94 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 836) hydrogen bonds : angle 2.73838 ( 2448) covalent geometry : bond 0.00280 (10056) covalent geometry : angle 0.53678 (13620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7757 (m110) REVERT: A 73 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7123 (mmm160) REVERT: A 76 ASP cc_start: 0.8136 (m-30) cc_final: 0.7820 (m-30) REVERT: B 46 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8121 (tttt) REVERT: B 55 LYS cc_start: 0.8612 (tttp) cc_final: 0.8384 (tttm) REVERT: B 73 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7660 (tpt170) REVERT: B 94 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7693 (mtt90) REVERT: C 73 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7652 (tpt170) REVERT: C 94 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7936 (ttm170) REVERT: D 72 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7757 (m110) REVERT: D 73 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7119 (mmm160) REVERT: D 76 ASP cc_start: 0.8167 (m-30) cc_final: 0.7853 (m-30) REVERT: E 46 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8121 (tttt) REVERT: E 55 LYS cc_start: 0.8594 (tttp) cc_final: 0.8371 (tttm) REVERT: E 73 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7659 (tpt170) REVERT: F 73 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7199 (mmm160) REVERT: F 94 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7780 (ttm170) REVERT: G 72 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7781 (m110) REVERT: G 73 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7111 (mmm160) REVERT: G 76 ASP cc_start: 0.8169 (m-30) cc_final: 0.7852 (m-30) REVERT: H 46 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8127 (tttt) REVERT: H 55 LYS cc_start: 0.8570 (tttp) cc_final: 0.8338 (tttm) REVERT: H 60 GLU cc_start: 0.7583 (tp30) cc_final: 0.7273 (tp30) REVERT: H 73 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7652 (tpt170) REVERT: I 73 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7202 (mmm160) REVERT: I 94 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7796 (ttm170) REVERT: J 72 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7653 (m110) REVERT: J 73 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7078 (mmm160) REVERT: J 76 ASP cc_start: 0.8274 (m-30) cc_final: 0.7921 (m-30) REVERT: K 46 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8127 (tttt) REVERT: K 55 LYS cc_start: 0.8603 (tttp) cc_final: 0.8377 (tttm) REVERT: K 73 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7636 (tpt170) REVERT: K 94 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7709 (mtt90) REVERT: L 73 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7183 (mmm160) REVERT: L 94 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7901 (ttm170) outliers start: 34 outliers final: 30 residues processed: 304 average time/residue: 0.2657 time to fit residues: 105.3970 Evaluate side-chains 305 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124605 restraints weight = 13887.984| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.10 r_work: 0.3245 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10056 Z= 0.143 Angle : 0.568 8.091 13620 Z= 0.300 Chirality : 0.032 0.135 1596 Planarity : 0.004 0.023 1812 Dihedral : 3.199 14.521 1356 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.31 % Allowed : 19.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.99 (0.21), residues: 1236 helix: 3.85 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.39 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 125 HIS 0.001 0.001 HIS H 78 PHE 0.004 0.001 PHE H 130 ARG 0.006 0.000 ARG H 94 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 836) hydrogen bonds : angle 2.79318 ( 2448) covalent geometry : bond 0.00316 (10056) covalent geometry : angle 0.56840 (13620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7775 (m110) REVERT: A 73 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7153 (mmm160) REVERT: A 76 ASP cc_start: 0.8154 (m-30) cc_final: 0.7818 (m-30) REVERT: B 46 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8150 (tttt) REVERT: B 55 LYS cc_start: 0.8638 (tttp) cc_final: 0.8358 (tttm) REVERT: B 73 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7681 (tpt170) REVERT: C 73 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7688 (tpt170) REVERT: C 94 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7951 (ttm110) REVERT: D 72 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7774 (m110) REVERT: D 73 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7166 (mmm160) REVERT: D 76 ASP cc_start: 0.8176 (m-30) cc_final: 0.7841 (m-30) REVERT: E 46 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8146 (tttt) REVERT: E 55 LYS cc_start: 0.8612 (tttp) cc_final: 0.8379 (tttm) REVERT: E 73 ARG cc_start: 0.8408 (mtp85) cc_final: 0.7673 (tpt170) REVERT: F 72 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: F 73 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7220 (mmm160) REVERT: F 94 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7798 (ttm170) REVERT: G 72 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7826 (m110) REVERT: G 73 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7148 (mmm160) REVERT: G 76 ASP cc_start: 0.8145 (m-30) cc_final: 0.7811 (m-30) REVERT: H 46 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8146 (tttt) REVERT: H 55 LYS cc_start: 0.8575 (tttp) cc_final: 0.8350 (tttm) REVERT: H 73 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7657 (tpt170) REVERT: I 73 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7213 (mmm160) REVERT: I 94 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7811 (ttm170) REVERT: J 72 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7727 (m110) REVERT: J 73 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7125 (mmm160) REVERT: J 76 ASP cc_start: 0.8260 (m-30) cc_final: 0.7906 (m-30) REVERT: K 46 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8151 (tttt) REVERT: K 55 LYS cc_start: 0.8603 (tttp) cc_final: 0.8381 (tttm) REVERT: K 73 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7659 (tpt170) REVERT: L 40 LEU cc_start: 0.8243 (mt) cc_final: 0.7638 (mt) REVERT: L 73 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7213 (mmm160) REVERT: L 94 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7872 (mtt90) outliers start: 35 outliers final: 30 residues processed: 297 average time/residue: 0.2630 time to fit residues: 101.5381 Evaluate side-chains 298 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain J residue 72 ASN Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN D 119 GLN F 119 GLN G 119 GLN I 119 GLN J 119 GLN L 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123690 restraints weight = 13920.106| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.10 r_work: 0.3228 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10056 Z= 0.153 Angle : 0.581 7.509 13620 Z= 0.306 Chirality : 0.033 0.182 1596 Planarity : 0.004 0.023 1812 Dihedral : 3.273 15.020 1356 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.50 % Allowed : 19.13 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.21), residues: 1236 helix: 3.76 (0.14), residues: 1008 sheet: None (None), residues: 0 loop : 0.27 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.002 0.001 HIS G 78 PHE 0.005 0.001 PHE H 130 ARG 0.006 0.000 ARG J 94 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 836) hydrogen bonds : angle 2.84554 ( 2448) covalent geometry : bond 0.00346 (10056) covalent geometry : angle 0.58086 (13620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.65 seconds wall clock time: 76 minutes 49.47 seconds (4609.47 seconds total)